Started running, putting on weight..

One of this things that is often said on here is Patience! 2 weeks is not a long time to see a long term difference. There are lots of reasons why you are showing an increase on the scales but you just have to keep in mind that your body needs time to adjust to a new routine. You know that you are doing something right by running. You are eating good food - not too much, logging all that you eat? Then it's just time (and a Zen attitude that's needed :-P)

Come back here in two months and give us an update. In fact I'm off to my post that I made a few weeks ago (on exactly this topic!) to say that I'm now seeing more weigh coming off and a leaner looking body emerging.

Is it better just to focus more on my diet?

yes.

or not add the running calories?

You might be overestimating the calorie burn, perhaps try eating back only 50% of the calories for a few weeks and see what happens. Although your first statement kind of implies you haven't been very on point with your diet, which would be the bigger issue.

(and it's not going to be muscle, I know that's going to get posted)

You just have started a new exercise...Let your body adjust to your new regime....Give it at least 2 months before making any decisions...continue with the great workout..:drinker:

first of all... why are you eating extra calories? Exercise is supposed to burn calories.... you eat your basic cals per day, not eat extra to make up for the exercise, and someone else said, you may be overcalculating how much you are burning.
I can tell you right now... MFP is NOT accurate for exercise cals, ridiculously over generous.
I can see plain as day why you are gaining.... STOP eating your exercise cals. End of story.
AND congrats on starting to run, its awesome!!!!!!

first of all... why are you eating extra calories? Exercise is supposed to burn calories.... you eat your basic cals per day, not eat extra to make up for the exercise, and someone else said, you may be overcalculating how much you are burning.
I can tell you right now... MFP is NOT accurate for exercise cals, ridiculously over generous.
I can see plain as day why you are gaining.... STOP eating your exercise cals. End of story.
AND congrats on starting to run, its awesome!!!!!!

She is not actually gaining....as someone else mentioned, she'd have to be overeating by 3500 calories in a week for that weight loss! Plus, when MFP gives us calorie counts you are SUPPOSED to eat back any exercise calories because of the already generous deficit. I eat 1500 calories if I don't work out and between 1600-2600 if I do...depending on the workout and I still lose.

Your muscles are probably retaining water from the new regimen. When I started running, I didn't lose for 3-4 weeks and then I dropped 17 pounds over the next 9 weeks. Now I just started lifting because the scale is stalled again but I'm not expecting to see a drop for a few more weeks because my muscles are very sore. Keep at it, stay focused, and if you're worried about an inaccurate calorie burn, buy a heart rate monitor....you can get a really good one for about 60$. I know MFP actually UNDERESTIMATED my burns meaning I wasn't eating ENOUGH when I started running (I was eating 200-400 calories less than what I should be).

Water retention.

I have gained 3 pounds from running, its all muscle in my calves and hamstrings. My legs look freaking awesome. I have a spectacular diet and I exercise so I put the scale away, it was freaking me out.

I gained loads of weight the first time I ever trained for a marathon- and completed it!
The problem was, I was over estimating the calorie burn.. I was thinking that when the treadmill said I'd burned 600+ calories, I could eat this back, but alas, when I invested in a really good heart rate monitor I found the calorie burn was around half of what the treadmill or cross trainer was telling me, grrr.
Also, I was seriously over doing it on the carbs- healthy carbs, but just far too many, I was constantly snacking on bowls of porridge, dried fruit, bananas, wholemeal bread.. Since Ive started strength training with a bit of cardio in the mornings, and changed the ratio of carbs and protein I've dropped over 15pounds, phew!!

I have gained 3 pounds from running, its all muscle in my calves and hamstrings. My legs look freaking awesome. I have a spectacular diet and I exercise so I put the scale away, it was freaking me out.

Um...I seriously doubt that. You can definately tone up those muscles and gain strength (at first) as they are put to use, but I seriously doubt the muscle gain as you say. You might have gained -some- stength in your legs as a result from running (I have) but not 3 lbs of muscle.

first of all... why are you eating extra calories? Exercise is supposed to burn calories.... you eat your basic cals per day, not eat extra to make up for the exercise, and someone else said, you may be overcalculating how much you are burning.
I can tell you right now... MFP is NOT accurate for exercise cals, ridiculously over generous.
I can see plain as day why you are gaining.... STOP eating your exercise cals. End of story.

I never eat the calories I burn during exercise! I hate that they add them on there. I consider those my weight loss calories. I always hear that you have to burn more than your eat to lose weight. If I eat my exercise calories, how can I loss weight? That's just how I see it. I know a lot of people do eat them. It's a personal thing.

With respect, it sounds like you are both misunderstanding how Myfitnesspal works. It gives a calorie goal with a calorie deficit already built into it, based on the information you entered when you signed up. MFP asks about your daily activity level, but does not include planned exercise or workouts like going to the gym, or running. It includes the activity from your normal day to day activities like your job, or household chores, or shopping etc. How active you are in general. That forms the basis of the calorie goal you get, and it is based on the assumption that any workouts you do, you log those and eat back the extra calories. Otherwise, MFP would have included all planned exercise and would have given you a higher calorie goal to start with. With the calorie goal MFP gives you, you can lose weight with no formal exercise. Of course, exercise is beneficial for lots of reasons, but that's besides the point. The vast majority of your daily calorie burn comes from your body's normal processes that keep you alive, and your normal daily activities. Those are really your "weight loss calories".

If, for example, you tell MFP you are sedentary, and then you go running 3 times a week, MFP will have given you a goal based on you being sedentary, and any additional exercise will be making your calorie deficit bigger. Sounds good, but having too large of a calorie deficit can be unhealthy and counter-productive over time. You risk losing far more lean mass than you would do otherwise, and you also risk messing up your hormones. This is especially true the closer you are to a healthy weight.

Now, a lot of people on MFP choose to customise their calorie goal to include all the activity and exercise they do. They don't "eat back" their exercise calories, but they end up with a larger calorie goal to start with.

It is a "personal thing" how big a calorie deficit you ultimately choose to have, some people decide to eat 500 calories a day and that's their choice. Doesn't mean it's a good idea. Understanding how MFP works is a good start, and giving blanket advice to stop eating exercise calories back is a really bad idea. In general, people who are obese and have larger amounts of fat stored can "get away with" large calorie deficits more than people who are closer to a healthy weight.

I started running 3x a week the last 2 weeks and my weight loss stopped after week 1 and now after week 2 i've put on a half a kilogram.

I'm using the a running app which allows me an extra 300 calories on the running days. Is it better just to focus more on my diet? or not add the running calories?

why, do you think you're not focusing enough on your diet?

are you running on an incline? I put on a little muscle weight when I run but there are hills where I am ...

From what I've heard a lot of the weight you lose in the first week is often water weight and the loss slows a bit for a couple of weeks and then picks up and you start to lose a little more steadily. I don't eat my calories back on days that I run, and eat back most of what I do on the days (mostly just extra protein) on days that I strength train.